Great plugin! Can you make it multisite-compatible? Two ideas that come to mind are to either append the site ID to the name of the file created, so multiple CSS files can be created/used, or make the .css file disabled when it's on a multisite install. I am using an older version of your plugin on my multisite installs, and it works like a charm, but I can't upgrade because the file would make the same CSS apply to all sites. It would be great if you could add this fix.
By the way, I just gave you a 5-star review, not that it should influence your priorities :)